Origin IGS: aagattcctttctgtgataaggtctaaaaaataaaagaaggcaggcgttagcgcatttcttcacatgataaattaaaaatgataaatggaaagtgagcgattgctgtgacttctgataggacttactcaaatgaagaggctaaaatgctgttttagccttgtatcttatggaaaagtaagagtaatgaaattgacctgatgtttaattattattgtaattataccatagaatgagcttaggaagcaagtcgggacggtgaatttcagagacggtttttcagccaaagcggcttgacaaaaagaaaaatcaagcgatgaacatttggtcacttgattttgagggctgc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gcagccctcaaaatcaagtgaccaaatgttcatcgcttgatttttctttttgtcaagccgctttggctgaaaaaccgtctctgaaattcaccgtcccgacttgcttcctaagctcattctatggtataattacaataataattaaacatcaggtcaatttcattactcttacttttccataagatacaaggctaaaacagcattttagcctcttcatttgagtaagtcctatcagaagtcacagcaatcgctcactttccatttatcatttttaatttatcatgtgaagaaatgcgctaacgcctgccttcttttattttttagaccttatcacagaaaggaatctt Mask Tandem Repeat Region ================================================ aagattcctttctgtgataaggtctaaaaaataaaagaaggcaggcgttagcgcatttcttcacatgataaattaaaaatgataaatggaaagtgagcgattgctgtgacttctgataggacttactcaaatgaagaggctaaaatgctgttttagccttgtatcttatggaaaagtaagagtaatgaaattgacctgatgtttaattattattgtaattataccatagaatgagcttaggaagcaagtcgggacggtgaatttcagagacggtttttcagccaaagcggcttgacaaaaagaaaaatcaagcgatgaacatttggtcacttgattttgagggctgc Find is-nt database================================================ Query_seq: SSA_0313:SSA_0314|SSA_0313:SSA_0314:Conserved uncharacterized protein:Nucleoside-diphosphate-sugar epimerase, putative:<-<-:308710..309056 347 aagattcctttctgtgataaggtctaaaaaataaaagaaggcaggcgttagcgcatttcttcacatgataaattaaaaatgataaatggaaagtgagcgattgctgtgacttctgataggacttactcaaatgaagaggctaaaatgctgttttagccttgtatcttatggaaaagtaagagtaatgaaattgacctgatgtttaattattattgtaattataccatagaatgagcttaggaagcaagtcgggacggtgaatttcagagacggtttttcagccaaagcggcttgacaaaaagaaaaatcaagcgatgaacatttggtcacttgattttgagggctgc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0313:SSA_0314|SSA_0313:SSA_0314:Conserved uncharacterized protein:Nucleoside-diphosphate-sugar epimerase, putative:<-<-:308710..309056 347 aagattcctttctgtgataaggtctaaaaaataaaagaaggcaggcgttagcgcatttcttcacatgataaattaaaaatgataaatggaaagtgagcgattgctgtgacttctgataggacttactcaaatgaagaggctaaaatgctgttttagccttgtatcttatggaaaagtaagagtaatgaaattgacctgatgtttaattattattgtaattataccatagaatgagcttaggaagcaagtcgggacggtgaatttcagagacggtttttcagccaaagcggcttgacaaaaagaaaaatcaagcgatgaacatttggtcacttgattttgagggctgc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0313:SSA_0314|SSA_0313:SSA_0314:Conserved uncharacterized protein:Nucleoside-diphosphate-sugar epimerase, putative:<-<-:308710..309056 347 aagattcctttctgtgataaggtctaaaaaataaaagaaggcaggcgttagcgcatttcttcacatgataaattaaaaatgataaatggaaagtgagcgattgctgtgacttctgataggacttactcaaatgaagaggctaaaatgctgttttagccttgtatcttatggaaaagtaagagtaatgaaattgacctgatgtttaattattattgtaattataccatagaatgagcttaggaagcaagtcgggacggtgaatttcagagacggtttttcagccaaagcggcttgacaaaaagaaaaatcaagcgatgaacatttggtcacttgattttgagggctgc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aagattcctttctgtgataaggtctaaaaaataaaagaaggcaggcgttagcgcatttcttcacatgataaattaaaaatgataaatggaaagtgagcgattgctgtgacttctgataggacttactcaaatgaagaggctaaaatgctgttttagccttgtatcttatggaaaagtaagagtaatgaaattgacctgatgtttaattattattgtaattataccatagaatgagcttaggaagcaagtcgggacggtgaatttcagagacggtttttcagccaaagcggcttgacaaaaagaaaaatcaagcgatgaacatttggtcacttgattttgagggctgc Predict ORF larger than 30AA ================================================ Protein_Len: 54 Strand: - Start: 169 End: 330 ........................................................................................................................................................................ P F T L T I F N V Q H K I I I T I I G Y F S S L F C T P V T F K L S P K E A L A A Q C F S F D L S S C K T M ................. Protein_Len: 43 Strand: - Start: 2 End: 130 . S E K R H Y P R F F L L L C A N A C K K V H Y I L F S L H F T L S Q Q S K Q Y S K S M ......................................................................................................................................................................................................................... aagattcctttctgtgataaggtctaaaaaataaaagaaggcaggcgttagcgcatttcttcacatgataaattaaaaatgataaatggaaagtgagcgattgctgtgacttctgataggacttactcaaatgaagaggctaaaatgctgttttagccttgtatcttatggaaaagtaagagtaatgaaattgacctgatgtttaattattattgtaattataccatagaatgagcttaggaagcaagtcgggacggtgaatttcagagacggtttttcagccaaagcggcttgacaaaaagaaaaatcaagcgatgaacatttggtcacttgattttgagggctgc Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ PromScan Matrix: RpoD-17 Strand: + Score: 84 Start: 190 End: 219 .............................................................................................................................................................................................ATTGACCTGATGTTTAATTATTATTGTAAT................................................................................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aagattcctttctgtgataaggtctaaaaaataaaagaaggcaggcgttagcgcatttcttcacatgataaattaaaaatgataaatggaaagtgagcgattgctgtgacttctgataggacttactcaaatgaagaggctaaaatgctgttttagccttgtatcttatggaaaagtaagagtaatgaaattgacctgatgtttaattattattgtaattataccatagaatgagcttaggaagcaagtcgggacggtgaatttcagagacggtttttcagccaaagcggcttgacaaaaagaaaaatcaagcgatgaacatttggtcacttgattttgagggctgc Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 61 HP_score: -5.8 Tail_Score: -3.54676 Start: 136 End: 160 Full_Region: ttttccataagatac aaggctaaaa cagca ttttagcctc ttcatttgagtaagt .......................................................................................................................................aaggctaaaacagcattttagcctc........................................................................................................................................................................................... TransTerm Strand: + Conf: 78 HP_score: -9.1 Tail_Score: -3.72788 Start: 138 End: 158 Full_Region: TTACTCAAATGAAGA GGCTAAAAT GCT GTTTTAGCC TTGTATCTTATGGAA .........................................................................................................................................GGCTAAAATGCTGTTTTAGCC............................................................................................................................................................................................. TransTerm Strand: - Conf: 70 HP_score: -8.4 Tail_Score: -3.34609 Start: 138 End: 158 Full_Region: ttccataagatacaa ggctaaaa cagca ttttagcc tcttcatttgagtaa .........................................................................................................................................ggctaaaacagcattttagcc............................................................................................................................................................................................. Find igs database================================================ Query_seq: SSA_0313:SSA_0314|SSA_0313:SSA_0314:Conserved uncharacterized protein:Nucleoside-diphosphate-sugar epimerase, putative:<-<-:308710..309056 347 aagattcctttctgtgataaggtctaaaaaataaaagaaggcaggcgttagcgcatttcttcacatgataaattaaaaatgataaatggaaagtgagcgattgctgtgacttctgataggacttactcaaatgaagaggctaaaatgctgttttagccttgtatcttatggaaaagtaagagtaatgaaattgacctgatgtttaattattattgtaattataccatagaatgagcttaggaagcaagtcgggacggtgaatttcagagacggtttttcagccaaagcggcttgacaaaaagaaaaatcaagcgatgaacatttggtcacttgattttgagggctgc Intra-Species Hit: Count: 1 Min: 1 Max: 347 Len: 347 Subject: NC_009009_SSA_0313_SSA_0314|Conserved uncharacterized protein:Nucleoside-diphosphate-sugar epimerase, putative|NEGATIVE:NEGATIVE|[308710,309056]|347 HSP 1 e-value: 0.0 bit: 688.0 Len: 347 Query Start:1 Query End:347 Subject Strand: POSITIVE Subject Start: 1 Subject End: 347 aagattcctttctgtgataaggtctaaaaaataaaagaaggcaggcgttagcgcatttcttcacatgataaattaaaaatgataaatggaaagtgagcgattgctgtgacttctgataggacttactcaaatgaagaggctaaaatgctgttttagccttgtatcttatggaaaagtaagagtaatgaaattgacctgatgtttaattattattgtaattataccatagaatgagcttaggaagcaagtcgggacggtgaatttcagagacggtttttcagccaaagcggcttgacaaaaagaaaaatcaagcgatgaacatttggtcacttgattttgagggctgc aagattcctttctgtgataaggtctaaaaaataaaagaaggcaggcgttagcgcatttcttcacatgataaattaaaaatgataaatggaaagtgagcgattgctgtgacttctgataggacttactcaaatgaagaggctaaaatgctgttttagccttgtatcttatggaaaagtaagagtaatgaaattgacctgatgtttaattattattgtaattataccatagaatgagcttaggaagcaagtcgggacggtgaatttcagagacggtttttcagccaaagcggcttgacaaaaagaaaaatcaagcgatgaacatttggtcacttgattttgagggctgc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAGAUUCCUUUCUGUGAUAAGGUCUAAAAAAUAAAAGAAGGCAGGCGUUAGCGCAUUUCUUCACAUGAUAAAUUAAAAAUGAUAAAUGGAAAGUGAGCGAUUGCUGUGACUUCUGAUAGGACUUACUCAAAUGAAGAGGCUAAAAUGCUGUUUUAGCCUUGUAUCUUAUGGAAAAGUAAGAGUAAUGAAAUUGACCUGAUGUUUAAUUAUUAUUGUAAUUAUACCAUAGAAUGAGCUUAGGAAGCAAGUCGGGACGGUGAAUUUCAGAGACGGUUUUUCAGCCAAAGCGGCUUGACAAAAAGAAAAAUCAAGCGAUGAACAUUUGGUCACUUGAUUUUGAGGGCUGC .......((((...(((((((..(((.........(((((...((((...((.(((((..((.(((...................)))))))))).))...))))....)))))..)))..)))).)))...)))).((((.(((.((((((((.........((((((......))))))....(((((((.(((.......(((((((....)))))))..((...((....(((.....)))...)).))..))).))))))))))))))).))).))))...(((((((..........(((((((((.(((.(.....).))).)))))))))..))))))) (-81.61) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCAGCCCUCAAAAUCAAGUGACCAAAUGUUCAUCGCUUGAUUUUUCUUUUUGUCAAGCCGCUUUGGCUGAAAAACCGUCUCUGAAAUUCACCGUCCCGACUUGCUUCCUAAGCUCAUUCUAUGGUAUAAUUACAAUAAUAAUUAAACAUCAGGUCAAUUUCAUUACUCUUACUUUUCCAUAAGAUACAAGGCUAAAACAGCAUUUUAGCCUCUUCAUUUGAGUAAGUCCUAUCAGAAGUCACAGCAAUCGCUCACUUUCCAUUUAUCAUUUUUAAUUUAUCAUGUGAAGAAAUGCGCUAACGCCUGCCUUCUUUUAUUUUUUAGACCUUAUCACAGAAAGGAAUCUU ..........(((((((((((...........)))))))))))((((((((((..((((.....))))........((((..(((((..........(((((((((.........((..(((((..((((((......)))))).......((......))...............)))))..))...(((((((((.....)))))))))........))))))))).....(((((.((..(((.((..((((.......(((.......)))........)))).))..)))((....)).)).)))))...)))))..))))......))))))))))..... (-65.26) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 927 140 91 231 182 NC_009009:SSA_0313|5end_Conserved_uncharacterized_protein_308619..308849_NEGATIVE 363 296 252 209 163 NC_009009:SSA_2331|5end_D-alanine_transfer_protein,_putative_2334964..2335194_NEGATIVE 357 297 252 77 19 NC_009009:SSA_0093|5end_V-type_sodium_ATPase,_subunit_D,_putative_94286..94516_POSITIVE 315 292 253 86 47 NC_009009:SSA_1478|5end_Transposase_ORF1,_putative_1482889..1483119_POSITIVE 312 58 11 219 151 NC_009009:SSA_2271|5end_hypothetical_protein_2272450..2272680_NEGATIVE 298 260 224 48 1 NC_009009:SSA_0498|5end_ABC-type_dipeptide/oligopeptide/nickel_transport_systems,_permease_components,_putative_497910..498140_POSITIVE 297 289 244 200 157 NC_009009:SSA_0061|5end_Tagatose_1,6-diphosphate_aldolase,_putative_62670..62900_POSITIVE 296 150 102 179 129 NC_009009:SSA_2157|5end_ATP-dependent_serine_protease,_putative_2158241..2158471_NEGATIVE 287 288 244 61 9 NC_009009:SSA_0510|5end_L-threonine-O-3-phosphate_decarboxylase,_putative_508523..508753_POSITIVE 286 125 97 38 7 NC_009009:SSA_2053|5end_hypothetical_protein_2057747..2057977_NEGATIVE 286 291 251 229 184 NC_009009:SSA_1197|5end_DNA_alkylation_repair_enzyme,_putative_1222699..1222929_NEGATIVE 283 288 244 159 102 NC_009009:SSA_1957|5end_Glycosyl_transferase_N-acetylglucosaminyltransferase,_putative_1954670..1954900_NEGATIVE 282 290 243 201 153 NC_009009:SSA_2281|5end_hypothetical_protein_2282370..2282600_NEGATIVE 282 171 135 223 184 NC_009009:SSA_0854|5end_hypothetical_protein_841335..841565_POSITIVE 282 260 218 161 121 NC_009009:SSA_0809|5end_Translation_initiation_inhibitor,_yjgF_family_/_endoribonuclease_L-PSP,_putative_791146..791376_POSITIVE 282 295 255 189 137 NC_009009:SSA_0494|5end_ABC-type_dipeptide/oligopeptide/nickel_transport_system,_ATPase_component,_putative_494407..494637_POSITIVE 280 279 233 160 120 NC_009009:SSA_0496|5end_Succinylglutamate_desuccinylase_/_Aspartoacylase_family,_putative_495946..496176_POSITIVE 278 45 5 191 139 NC_009009:SSA_1436|5end_hypothetical_protein_1443125..1443355_NEGATIVE 275 282 243 208 163 NC_009009:SSA_1393|5end_hypothetical_protein_1408773..1409003_NEGATIVE 274 69 23 210 165 NC_009009:SSA_1561|5end_Ribonuclease_III,_putative_1565883..1566113_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 357 297 252 80 22 NC_009009:SSA_0092|3end_V-type_sodium_ATPase,_subunit_B,_putative_94369..94519_POSITIVE 312 58 11 92 24 NC_009009:SSA_2272|3end_hypothetical_protein_2272577..2272727_NEGATIVE 298 277 234 59 12 NC_009009:SSA_2168|3end_Glycerol-3-phosphate_dehydrogenase_[NAD(P)+],_putative_2168563..2168713_POSITIVE 298 140 91 90 29 NC_009009:SSA_1453|3end_hypothetical_protein_1459897..1460047_NEGATIVE 298 260 224 55 8 NC_009009:SSA_0497|3end_Nickel_ABC_transporter,_putative_497997..498147_POSITIVE 290 139 92 76 25 NC_009009:SSA_1306|3end_Trk_transporter_NAD+_binding_protein-K+_transport,_putative_1324245..1324395_NEGATIVE 276 168 133 88 50 NC_009009:SSA_0020|3end_Ribose-phosphate_pyrophosphokinase_1,_putative_26609..26759_POSITIVE 274 69 23 88 43 NC_009009:SSA_1562|3end_hypothetical_protein_1566005..1566155_NEGATIVE 274 289 248 55 18 NC_009009:SSA_1409|3end_DTDP-glucose-4,6-dehydratase,_putative_1421209..1421359_NEGATIVE 272 288 244 150 97 NC_009009:SSA_1666|3end_Collagen-binding_surface_protein,_putative_1665375..1665525_NEGATIVE 272 324 281 109 60 NC_009009:SSA_0986|3end_Choline_transporter,_putative_989081..989231_POSITIVE 269 272 232 76 31 NC_009009:SSA_2081|3end_hypothetical_protein_2085490..2085640_POSITIVE 269 296 262 54 25 NC_009009:SSA_0581|3end_Conserved_uncharacterized_protein_573774..573924_POSITIVE 265 278 234 74 31 NC_009009:SSA_0204|3end_Nisin_biosynthesis_two-component_response_transcriptional_regulator_nisR,_putative_202835..202985_POSITIVE 264 288 249 138 101 NC_009009:SSA_1956|3end_ABC-type_Fe-S_cluster_assembly_transporter,_ATPase_component,_putative_1952644..1952794_NEGATIVE 264 285 245 60 18 NC_009009:SSA_0197|3end_Dihydropteroate_synthase,_putative_196979..197129_POSITIVE 263 294 255 82 50 NC_009009:SSA_0931|3end_hypothetical_protein_941335..941485_POSITIVE 263 129 82 103 50 NC_009009:SSA_0900|3end_Tetratricopeptide_repeat_(TPR)_family_protein_892377..892527_POSITIVE 262 288 241 117 72 NC_009009:SSA_2068|3end_Superfamily_I_DNA_and_RNA_helicases,_putative_2070931..2071081_NEGATIVE 261 292 256 132 98 NC_009009:SSA_2285|3end_hypothetical_protein_2287825..2287975_POSITIVE